Nanostructured chitosan (CS) and a chitosan-Zn based (Zn-CS) complex have been synthesized and simultaneously deposited on cotton fabrics using ultrasound. SEM measurements revealed that the coating consists of nanoparticles (NPs) of ca. 40 nm in diameter, homogeneously dispersed along the yarns. XANES studies pointed out that the complex consisted of a less than 2.1 nm ZnO core to which the chitosan was bonded. Additionally, FTIR measurements indicated the in situ formation of a Zn-CS complex which is the only deposited material on the cotton surface. The antibacterial properties of the CS and Zn-CS coated textiles were tested against Gram positive and Gram negative bacteria species. More than two-fold increase of the antibacterial activity of Zn-CS NP coated textiles was detected as compared to the fabrics treated with the sonochemically synthesized CS NPs alone. The sonochemical technique appears to be a suitable method for producing organic NPs of soluble compounds, without loss of their intrinsic properties, i.e. the antimicrobial activity of chitosan. Moreover, hybrid nanoorganometallic particles were simultaneously synthesized and deposited on cotton sonochemically.